Mine is vertical, they way it was intended to be with the gray stand, and the clear, circular stand that supports the gray stand. It actually works. I put my Wii horizontally when I play GC/VC games because the controller ends won't fit under the rack.

when im in a retro mood i put it on its side as it looks a bit like the nes when im a techno cool mood i put it vertically, most of the time! and whats the point in having a stand if ur not gona use it the wii doesnt look right without it